[gmx-users] Re: No such moleculetype SOL

Jonathan Saboury jsabou1 at gmail.com
Mon Sep 23 04:10:13 CEST 2013

>Then something is wrong with the way you've done it, because the job of
>is to define the [moleculetype] SOL and all its relevant parameters.

Hm...not sure what the matter is. Added a forcefield as well as spc.itp to
the .top file made by acpype. Still getting the error "Fatal error: No such
moleculetype SOL"

Here is a list of commands and explanations of what I did:
Here is the .top: http://pastebin.com/raw.php?i=LzCANQZw
Here are the files I am using: http://www.sendspace.com/file/5ps0i1

It is important to note that genbox did not add the amount of cyclohexanes
added to system in the .top (it did do it for the waters though). Perhaps
that is a bug?

>You need a parent force field that defines all the bonded and nonbonded
>interactions in the system.  Whether or not this is one that comes with
>or one you design yourself, you still have to satisfy all of the internal
>mechanics (see Chapter 5).  Whether or not there is a protein is completely
>irrelevant; force fields do much more than just proteins.

I see, interesting. Added it to the .top :)

>Well, PRODRG parameters are pretty low-quality anyway, but it's a
>example for doing a tutorial rather than trying to teach people how to use
>external software ;)

As you know I am using acpype, is it any better? What do you use?

Thank you for the help Justin, it is extremely appreciated :)

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